#GalaxyFill: A program for filling up the missing part of protein structure
##0. Remark The GalaxyFill distribution version supports only Linux 64-bit OS and binary files compiled with serial option. Linux 32-bit OS or binary files compiled with MPI option are not supported.
##1. Installation
- Download the GalaxyFill program
- Download a copy of GalaxyFill
- https://github.com/seoklab/GalaxyFill
- https://github.com/seoklab/GalaxyFill/archive/master.zip * Or, clone the GalaxyFill git repository
- git clone https://github.com/seoklab/GalaxyFill.git
- Unzip and place the downloaded files
- unzip GalaxyFill.zip
- mv GalaxyFill $GALAXY_HOME
(example: GALAXY_HOME=/applic/GalaxyFill)
- Check the downloaded files
- There should exist:
- bin: directory for executables
There should be build_initial_model and GalaxyFill - data: directory for data files
- examples: directory for example files
- Set environment variable
- export GALAXY_HOME=$GALAXY_HOME
(example: export GALAXY_HOME=/applic/GalaxyFill)
- export GALAXY_HOME=$GALAXY_HOME
##2. How to use GalaxyFill
- Prepare the input protein structure in PDB format
- You have to provide a protein structure in the PDB file format for structure refinement. Gaps (or chain breaks) are highly prohibited in the middle of the initial protein structure.
- Run GalaxyFill
- Usage: $GALAXY_HOME/bin/GalaxyFill [-h] [-p INPUT PDB File] [-s INPUT FASTA File]
- Input arguments and options:
- -p or –pdb : Input protein structure file in PDB format (mendatory)
- -s or –seq : Input protein sequence file in FASTA format (mendatory)
- -o or –out : Output protein structure file name (optional, default=${Input PDB prefix}_fill.pdb)
- -t or –title : Running title for GalaxyFill (optional, default=${Input PDB prefix})
- Output of GalaxyFill
- The final refined model will be ${Input PDB prefix}_fill.pdb or designated by “-o/–out” option
##3. Release log
- 10 Apr 2016: Local energy optimization on the filled residues
- 09 Apr 2016: Added optional arguments: -o and -t
- 01 Feb 2016: The first release of GalaxyFill
##4. References
- E. A. Coutsias, C. Seok, M. P. Jacobson, and K. A. Dill, A Kinematic View of Loop Closure, J. Comput. Chem. 25, 510-528 (2004).
##5. Contact
- chaok@snu.ac.kr
- compbio.galaxy@gmail.com